Most mammals have two cone types, namely S- and M-cones. They diverge in their sensitivity to different wavelengths of light, based on their expression of different light-sensitive proteins: S-opsin for blue light and M-opsin for green light. The purpose of this research project is to identify genetic differences in cones and, more specifically, to find genes that are involved in cone synapse formation. Until now, cones have been classified mostly by the opsin they express. Recent findings in our laboratory point to the existence of additional genetic differences. Normally, the dendrites of the S-cone bipolar cell (SCBC), exclusively contact S-cones. However, genetic disruption of the normal S- and M-opsin expression pattern in different knockout mice fails to alter that specific connection. To find the molecular signatures of S- and M-cones, we have turned to single cell RNA-sequencing. For this study, we used the 13-lined ground squirrel that, in contrast to mouse, is diurnal and has a cone-dominated retina. The two cone types are morphologically indistinguishable, so we developed a protocol to dissociate and label live cells with an antibody targeting the extracellular domain of S-opsin. We then manually collected single cells for next-generation sequencing. The analysis revealed differentially expressed genes. Among others, we identified S-cone specific cell-adhesion molecules that are known to play roles in synapse assembly in the brain. Using Single Molecule Fluorescence In Situ Hybridization (smFISH) technique, we were able to verify the expression of some candidate genes. The outcome of this study can help to understand circuit formation in the retina and synapse assembly in the nervous system. For clinical applications, this can be an important starting point for future studies that aim to replace or rewire photoreceptors in retinal degenerative diseases.